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Abstract
Epigenetic alleles (epialleles) are heritable loci that vary in chromatin state and offer an additional source of variation that can affect phenotypic diversity beyond changes to DNA sequence. They can affect gene expression and are both mitotically and meiotically heritable in plants making epialleles a potential mechanism for crop improvement. Previous research has determined the rate at which epialleles arise, however, it is unknown how long they are maintained and how they are inherited. Before investing resources into developing targeted epialleles in crops, it is important that epialleles are predictably inherited to offspring and stable within the plant. My work focuses on further understanding and visualizing the stability and heritability of epialleles across generations and within an organism. First, using consecutive generations of two Arabidopsis thaliana mutation accumulation (MA) lines, I computed the transgenerational stability of epialleles via self-fertilization. About 99.998% of methylated regions are stably inherited to the next generation. Additionally, by crossing individuals from two genetically-identical but epigenetically-distinct MA lines, I showed that most parental epialleles are inherited to offspring in a Mendelian manner. Next, I used eight terminal branches of a 350-year-old wild Populus trichocarpa tree to determine epiallele stability within an organism. I computed the somatic single site epimutation and epiallele mutation rates per-year, which are 100-1000x lower than in the per-generation rates in A. thaliana MA lines. I also demonstrated that, except for rare examples, gene expression level and nearby epialleles are independent. Finally, I developed several pieces of software that allow for epigenetics visualization. This software has been essential in identifying, validating, describing, and presenting epialleles. Taken together, my research provides strong evidence and clear, visual examples of both transgenerational and intra-organismal epiallele stability, a fact often under-appreciated by those in the field, and lays the groundwork for engineering epialleles in crops.